Contacts of the helix formed by residues 299 - 311 (chain K) in PDB entry 7C97
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 299 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56G T 3.5 17.7 + - - +
57G T 2.5 35.1 + - - +
266K SER* 4.3 15.2 - - - -
269K CYS* 4.0 11.7 - - - -
298K LYS* 1.3 73.2 - - - +
300K LEU* 1.3 67.3 + - - +
301K THR 3.3 1.6 - - - -
302K GLU* 3.6 7.1 + - - +
303K ILE* 3.6 19.9 + - - +
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Residues in contact with LEU 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G T 6.2 4.1 - - + +
58G G 6.1 2.7 - - - +
286K GLU* 3.3 31.0 - - + +
289K LEU* 5.9 2.7 - - + -
299K SER* 1.3 77.8 - - - +
301K THR* 1.3 70.3 + - - +
302K GLU 3.2 0.9 + - - -
303K ILE* 3.5 28.9 - - + +
304K LYS* 3.6 23.7 + - + +
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Residues in contact with THR 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298K LYS* 5.0 12.2 - - - +
299K SER 3.3 1.6 - - - +
300K LEU* 1.3 84.4 - - - +
302K GLU* 1.3 73.1 + - - +
304K LYS* 3.2 22.1 + - + +
305K ASP* 3.5 21.5 + - - +
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Residues in contact with GLU 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G T 4.8 7.1 + - - +
262K LEU* 5.6 3.0 - - + +
263K THR* 4.4 15.5 - - + +
266K SER* 3.4 31.2 - - - +
298K LYS* 2.6 39.6 - - - +
299K SER 3.6 0.6 + - - +
300K LEU 3.2 0.6 - - - -
301K THR* 1.3 90.1 + - - +
303K ILE* 1.3 61.8 + - - +
304K LYS 3.1 1.8 - - - -
305K ASP* 4.9 2.1 - - - +
306K VAL* 3.0 27.7 + - - +
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Residues in contact with ILE 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262K LEU* 6.1 0.7 - - + -
266K SER* 4.9 4.0 - - - +
270K LEU* 3.8 37.5 - - + -
281K LEU* 5.9 9.4 - - + +
286K GLU* 5.9 1.3 - - + -
289K LEU* 3.6 31.6 - - + -
299K SER 3.6 13.0 - - - +
300K LEU* 3.5 21.1 - - + +
302K GLU* 1.3 77.3 - - - +
304K LYS* 1.3 64.8 + - + +
306K VAL* 3.3 15.4 - - + +
307K LEU* 3.1 33.6 - - + +
314K LEU* 5.1 14.6 - - + -
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Residues in contact with LYS 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286K GLU* 5.6 3.1 - - - -
300K LEU* 3.7 23.3 - - + +
301K THR* 3.3 14.6 - - + +
302K GLU 3.1 0.6 - - - -
303K ILE* 1.3 83.1 - - + +
305K ASP* 1.3 69.2 + - - +
307K LEU* 3.3 31.5 - - + +
308K ALA* 3.3 7.8 + - - +
314K LEU* 4.9 20.0 - - + -
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Residues in contact with ASP 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K THR* 3.5 22.6 + - - +
302K GLU* 4.0 2.4 + - - +
304K LYS* 1.3 84.0 - - - +
306K VAL* 1.3 60.8 + - - +
308K ALA* 3.7 6.6 - - - +
309K SER* 2.9 32.6 + - - -
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Residues in contact with VAL 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260K LEU* 3.8 44.6 - - + +
262K LEU* 4.5 20.0 - - + -
281K LEU* 6.2 2.9 - - + -
302K GLU 3.0 26.2 + - - +
303K ILE* 3.3 15.7 - - - +
305K ASP* 1.3 79.3 - - - +
307K LEU* 1.3 63.6 + - + +
309K SER* 2.7 19.5 + - - +
310K ARG* 3.5 14.6 - - - +
312K LEU* 4.9 2.7 - - - +
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Residues in contact with LEU 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K LEU* 5.3 15.3 - - + -
303K ILE* 3.1 29.2 - - + +
304K LYS* 3.3 18.6 - - + +
306K VAL* 1.3 82.9 - - + +
308K ALA* 1.3 79.4 + - + +
309K SER 3.2 2.9 + - - -
311K GLY 3.5 2.6 + - - -
312K LEU* 2.6 64.9 + - + +
313K SER* 3.8 22.9 - - - +
314K LEU* 4.2 21.5 - - + +
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Residues in contact with ALA 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304K LYS 3.3 15.1 + - - +
305K ASP* 3.5 8.7 + - - +
307K LEU* 1.3 86.7 - - + +
309K SER* 1.3 58.9 + - - +
311K GLY* 4.5 3.2 + - - -
312K LEU 4.1 4.3 - - - +
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Residues in contact with SER 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305K ASP 2.9 14.5 + - - -
306K VAL* 2.7 28.4 + - - +
307K LEU 3.2 0.2 - - - -
308K ALA* 1.3 79.9 - - - +
310K ARG* 1.3 66.2 + - - +
311K GLY 3.5 0.8 + - - -
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Residues in contact with ARG 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603F ARG* 6.1 0.4 - - - +
252K ILE* 2.9 34.7 - - + +
255K ARG* 4.9 18.7 - - - +
259K ASP* 3.3 25.7 + - - -
260K LEU* 3.6 37.6 - - - +
306K VAL* 3.5 12.3 - - - +
307K LEU 3.8 1.8 + - - -
309K SER* 1.3 90.4 - - - +
311K GLY* 1.3 59.0 + - - +
312K LEU* 4.9 4.5 - - + -
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Residues in contact with GLY 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K ASP* 5.2 2.9 - - - +
252K ILE* 4.0 13.0 - - - +
307K LEU 3.5 2.2 + - - -
308K ALA 4.5 2.3 + - - -
309K SER 3.5 3.4 + - - +
310K ARG* 1.3 80.3 - - - +
312K LEU* 1.3 66.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il